6e23c5700ff2d2d1ade34de13cddfd3c2bf8ec3a
wong
  Mon Nov 14 17:00:42 2011 -0800
reworked the makefiles to allow for a split pipeline
diff --git src/inc/common.mk src/inc/common.mk
index 43083e8..5a4fef6 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -1,205 +1,215 @@
 CC=gcc
 # to build on sundance: CC=gcc -mcpu=v9 -m64
 ifeq (${COPT},)
     COPT=-O -g
 endif
 ifeq (${CFLAGS},)
     CFLAGS=
 endif
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
 
 #global external libraries 
 L=
 
 # pthreads is required
 L+=-pthread
 
 # autodetect if openssl is installed
 ifeq (${SSLDIR},)
   SSLDIR = /usr/include/openssl
 endif
 ifeq (${USE_SSL},)
   ifneq ($(wildcard ${SSLDIR}),)
      USE_SSL=1
   endif
 endif
 
 
 # libssl: disabled by default
 ifeq (${USE_SSL},1)
     L+=-lssl -lcrypto
     HG_DEFS+=-DUSE_SSL
 endif
 
 # autodetect where png is installed
 ifeq (${PNGLIB},)
   ifneq ($(wildcard /usr/lib64/libpng.a),)
       PNGLIB=/usr/lib64/libpng.a
   endif
 endif
 ifeq (${PNGLIB},)
   ifneq ($(wildcard /usr/lib/libpng.a),)
       PNGLIB=/usr/lib/libpng.a
   endif
 endif
 ifeq (${PNGLIB},)
   PNGLIB=-lpng
 endif
 
 L+=${PNGLIB}
 HG_INC+=${PNGINCL}
 
 # 32-bit color enabled by default
 ifneq (${COLOR32},0)
     HG_DEFS+=-DCOLOR32
 endif
 
 # autodetect local installation of samtools:
 ifeq (${SAMDIR},)
   SAMDIR = /hive/data/outside/samtools/svn_${MACHTYPE}/samtools
   ifneq ($(wildcard ${SAMDIR}),)
      KNETFILE_HOOKS=1
   endif
 endif
 ifeq (${USE_BAM},)
   ifneq ($(wildcard ${SAMDIR}),)
      USE_BAM=1
   endif
 endif
 
 # libbam (samtools, and Angie's KNETFILE_HOOKS extension to it): disabled by default
 ifeq (${USE_BAM},1)
     ifeq (${SAMINC},)
         SAMINC = ${SAMDIR}
     endif
     ifeq (${SAMLIB},)
         SAMLIB = ${SAMDIR}/libbam.a
     endif
     HG_INC += -I${SAMINC}
     L+=${SAMLIB}
     HG_DEFS+=-DUSE_BAM
     ifeq (${KNETFILE_HOOKS},1)
 	HG_DEFS+=-DKNETFILE_HOOKS
     endif
 endif
 
 # As we do for bam/samtools, so do for tabix.  autodetect local installation:
 ifeq (${TABIXDIR},)
   TABIXDIR = /hive/data/outside/tabix/tabix-0.2.3/${MACHTYPE}
   ifneq ($(wildcard ${TABIXDIR}),)
      KNETFILE_HOOKS=1
   endif
 endif
 ifeq (${USE_TABIX},)
   ifneq ($(wildcard ${TABIXDIR}),)
      USE_TABIX=1
   endif
 endif
 
 # libtabix and Angie's KNETFILE_HOOKS extension to it: disabled by default
 ifeq (${USE_TABIX},1)
     ifeq (${TABIXINC},)
         TABIXINC = ${TABIXDIR}
     endif
     ifeq (${TABIXLIB},)
         TABIXLIB = ${TABIXDIR}/libtabix.a
     endif
     HG_INC += -I${TABIXINC}
     L+=${TABIXLIB} -lz
     HG_DEFS+=-DUSE_TABIX
     ifeq (${KNETFILE_HOOKS},1)
 	HG_DEFS+=-DKNETFILE_HOOKS
     endif
 endif
 
 SYS = $(shell uname -s)
 
 ifeq (${HG_WARN},)
   ifeq (${SYS},Darwin)
       HG_WARN = -Wall -Wno-unused-variable
       HG_WARN_UNINIT=
   else
     ifeq (${SYS},SunOS)
       HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
       HG_WARN_UNINIT=-Wuninitialized
     else
       HG_WARN = -Wall -Werror -Wformat -Wimplicit -Wreturn-type
       # HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
       HG_WARN_UNINIT=-Wuninitialized
     endif
   endif
   # -Wuninitialized generates a warning without optimization
   ifeq ($(findstring -O,${COPT}),-O)
      HG_WARN += ${HG_WARN_UNINIT}
   endif
 endif
 
 # this is to hack around many make files not including HG_WARN in
 # the link line
 CFLAGS += ${HG_WARN}
 
 ifeq (${SCRIPTS},)
     SCRIPTS=${HOME}/bin/scripts
 endif
 ifeq (${CGI_BIN},)
     CGI_BIN=/usr/local/apache/cgi-bin
 endif
 ifeq (${DOCUMENTROOT},)
     DOCUMENTROOT=/usr/local/apache/htdocs
 endif
 ifeq (${BINDIR},)
     BINDIR = ${HOME}/bin/${MACHTYPE}
 endif
 ifeq (${ENCODE_PIPELINE_BIN},)
     ENCODE_PIPELINE_BIN=/cluster/data/encode/pipeline/bin
 endif
 
 MKDIR=mkdir -p
 ifeq (${STRIP},)
    STRIP=strip
 endif
 CVS=cvs
 GIT=git
 
 # portable naming of compiled executables: add ".exe" if compiled on 
 # Windows (with cygwin).
 ifeq (${OS}, Windows_NT)
   AOUT=a
   EXE=.exe
 else
   AOUT=a.out
   EXE=
 endif
 
 # location of stringify program
 STRINGIFY = ${DESTDIR}${BINDIR}/stringify
 
 #Lowelab defines
 #The lowelab specific code will be included in compilation if the following conditions are satistied
 LOWELAB_WIKI_DEF=
 LOWELAB_DEF=
 ifdef LOWELAB
     LOWELAB_WIKI=1
     LOWELAB_DEF=-DLOWELAB
 endif
 ifdef LOWELAB_WIKI
     LOWELAB_WIKI_DEF=-DLOWELAB_WIKI
 endif
 LOWELAB_DEFS=${LOWELAB_DEF} ${LOWELAB_WIKI_DEF}
 
 ifdef LOWELAB
     ifeq (${SCRIPTS},/cluster/bin/scripts)
         SCRIPTS=${HOME}/scripts
     endif
     ifeq (${CGI_BIN},/usr/local/apache/cgi-bin)
         CGI_BIN=/www/cgi-bin
     endif
     ifeq (${DOCUMENTROOT},/usr/local/apache/htdocs)
         DOCUMENTROOT=/www/browser-docs
     endif
 endif
 
+#ENCODE COMMON VARIABLES
+CONFIG_FILES = \
+	fields.ra \
+	labs.ra
+CV = cv.ra
+CVDIR=${HOME}/kent/src/hg/makeDb/trackDb/cv/alpha
+PIPELINE_PATH=/hive/groups/encode/dcc/pipeline
+CONFIG_DIR = ${PIPELINE_PATH}/${PIPELINE_DIR}/config
+ENCODEDCC_DIR = ${PIPELINE_PATH}/downloads/encodeDCC
+
 %.o: %.c
 	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<